[2024-01-25 18:53:21,045] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:21,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:21,046] [INFO] DQC Reference Directory: /var/lib/cwl/stga876f8fc-9728-4205-ba7d-987361d6a1b5/dqc_reference
[2024-01-25 18:53:22,149] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:22,149] [INFO] Task started: Prodigal
[2024-01-25 18:53:22,150] [INFO] Running command: gunzip -c /var/lib/cwl/stg94459d9a-d8b3-4bf5-9737-09a3ae78793d/GCF_000964005.1_WiARP1.0_genomic.fna.gz | prodigal -d GCF_000964005.1_WiARP1.0_genomic.fna/cds.fna -a GCF_000964005.1_WiARP1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:39,685] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:39,685] [INFO] Task started: HMMsearch
[2024-01-25 18:53:39,685] [INFO] Running command: hmmsearch --tblout GCF_000964005.1_WiARP1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga876f8fc-9728-4205-ba7d-987361d6a1b5/dqc_reference/reference_markers.hmm GCF_000964005.1_WiARP1.0_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:39,916] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:39,917] [INFO] Found 6/6 markers.
[2024-01-25 18:53:39,954] [INFO] Query marker FASTA was written to GCF_000964005.1_WiARP1.0_genomic.fna/markers.fasta
[2024-01-25 18:53:39,954] [INFO] Task started: Blastn
[2024-01-25 18:53:39,955] [INFO] Running command: blastn -query GCF_000964005.1_WiARP1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stga876f8fc-9728-4205-ba7d-987361d6a1b5/dqc_reference/reference_markers.fasta -out GCF_000964005.1_WiARP1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:41,043] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:41,045] [INFO] Selected 14 target genomes.
[2024-01-25 18:53:41,046] [INFO] Target genome list was writen to GCF_000964005.1_WiARP1.0_genomic.fna/target_genomes.txt
[2024-01-25 18:53:41,060] [INFO] Task started: fastANI
[2024-01-25 18:53:41,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg94459d9a-d8b3-4bf5-9737-09a3ae78793d/GCF_000964005.1_WiARP1.0_genomic.fna.gz --refList GCF_000964005.1_WiARP1.0_genomic.fna/target_genomes.txt --output GCF_000964005.1_WiARP1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:56,324] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:56,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga876f8fc-9728-4205-ba7d-987361d6a1b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:56,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga876f8fc-9728-4205-ba7d-987361d6a1b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:56,334] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:53:56,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:56,334] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Williamsia herbipolensis	strain=ARP1	GCA_000964005.1	1603258	1603258	type	True	100.0	1556	1557	95	conclusive
Williamsia phyllosphaerae	strain=CCM 7855	GCA_014635305.1	885042	885042	type	True	82.3631	1031	1557	95	below_threshold
Williamsia maris	strain=DSM 44693	GCA_024171815.1	72806	72806	type	True	82.2789	1064	1557	95	below_threshold
Williamsia serinedens	strain=DSM 45037	GCA_024171725.1	391736	391736	type	True	81.1363	937	1557	95	below_threshold
Williamsia deligens	strain=DSM 44902	GCA_024171765.1	321325	321325	type	True	81.1099	937	1557	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	79.2113	582	1557	95	below_threshold
Gordonia rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	79.192	584	1557	95	below_threshold
Williamsia sterculiae	strain=CPCC 203464	GCA_900156495.1	1344003	1344003	type	True	78.7805	606	1557	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_024734075.1	2665643	2665643	type	True	78.6744	562	1557	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_009828195.1	2665643	2665643	type	True	78.6212	554	1557	95	below_threshold
Prescottella agglutinans	strain=CCTCC AB2014297	GCA_004011865.1	1644129	1644129	type	True	78.212	520	1557	95	below_threshold
Rhodococcus wratislaviensis	strain=NCTC13229	GCA_900455735.1	44752	44752	suspected-type	True	77.8543	514	1557	95	below_threshold
Rhodococcus pseudokoreensis	strain=R79	GCA_017068395.1	2811421	2811421	type	True	77.8491	535	1557	95	below_threshold
Rhodococcus wratislaviensis	strain=NBRC 100605	GCA_000583735.1	44752	44752	suspected-type	True	77.7138	531	1557	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:56,336] [INFO] DFAST Taxonomy check result was written to GCF_000964005.1_WiARP1.0_genomic.fna/tc_result.tsv
[2024-01-25 18:53:56,336] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:56,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:56,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga876f8fc-9728-4205-ba7d-987361d6a1b5/dqc_reference/checkm_data
[2024-01-25 18:53:56,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:56,383] [INFO] Task started: CheckM
[2024-01-25 18:53:56,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000964005.1_WiARP1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000964005.1_WiARP1.0_genomic.fna/checkm_input GCF_000964005.1_WiARP1.0_genomic.fna/checkm_result
[2024-01-25 18:55:24,296] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:24,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:24,332] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:24,332] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:24,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000964005.1_WiARP1.0_genomic.fna/markers.fasta)
[2024-01-25 18:55:24,333] [INFO] Task started: Blastn
[2024-01-25 18:55:24,333] [INFO] Running command: blastn -query GCF_000964005.1_WiARP1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stga876f8fc-9728-4205-ba7d-987361d6a1b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000964005.1_WiARP1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:25,974] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:25,977] [INFO] Selected 15 target genomes.
[2024-01-25 18:55:25,977] [INFO] Target genome list was writen to GCF_000964005.1_WiARP1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:25,985] [INFO] Task started: fastANI
[2024-01-25 18:55:25,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg94459d9a-d8b3-4bf5-9737-09a3ae78793d/GCF_000964005.1_WiARP1.0_genomic.fna.gz --refList GCF_000964005.1_WiARP1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000964005.1_WiARP1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:42,692] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:42,702] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:42,702] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000964005.1	s__Williamsia_A herbipolensis	100.0	1556	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	95.03	95.03	0.89	0.89	2	conclusive
GCF_014635305.1	s__Williamsia_A phyllosphaerae	82.3668	1030	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462415.1	s__Williamsia_A sp016462415	82.2355	959	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018474015.1	s__Williamsia_A sp018474015	80.1199	715	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344155.1	s__Gordonia paraffinivorans	79.5548	597	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
GCF_000327325.1	s__Gordonia rubripertincta	79.2301	580	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCA_013348785.1	s__Gordonia sp013348785	78.802	474	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156495.1	s__Williamsia_B sterculiae	78.7876	605	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149015.1	s__Gordonia lacunae	78.7795	614	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828195.1	s__Gordonia sp009828195	78.65	548	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298195.1	s__Gordonia rhizosphera	78.6293	562	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700145.1	s__Gordonia sp002700145	78.3579	565	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011865.1	s__Rhodococcus agglutinans	78.2357	516	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017068395.1	s__Rhodococcus sp002165735	77.8466	534	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.37	95.32	0.78	0.69	5	-
GCF_900455735.1	s__Rhodococcus wratislaviensis	77.8252	518	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.31	98.94	0.95	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:42,703] [INFO] GTDB search result was written to GCF_000964005.1_WiARP1.0_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:42,704] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:42,707] [INFO] DFAST_QC result json was written to GCF_000964005.1_WiARP1.0_genomic.fna/dqc_result.json
[2024-01-25 18:55:42,707] [INFO] DFAST_QC completed!
[2024-01-25 18:55:42,708] [INFO] Total running time: 0h2m22s